A new European subclade of K1a1b1


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YDNA:
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PostPosted: Fri Jul 05, 2013 8:26 am
From the paper of Cardoso posted by Gail T on anthrogenica we have:

JX297145 is interesting because probably is a new subclade of K1a1b1, perhaps with the Coding Region mutation 5742T. It has also the mutations 3107del, 16278T and a back mutation in 16224T!, already known from the Basque country.
We have on Mitosearch a Russian (from German descent), unfortunately tested only for HVRI, with 16224C.
Also this subclade of K1a1b1 is then European, like all the others, except the discussed Jewish K1a1b1a.

Posts: 2341
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
R- Z2110 (KV7Y2)
MtDNA:
K1a1b1e/HQ176413
PostPosted: Fri Jul 05, 2013 8:39 am
On the Ian Logan spreadsheet we already have

14. DQ200804(Basque) Gonzalez K1a1b1 13-JUN-2006 A73G A263G 315.1C C497T A750G T1189C A1438G A1811G A2706G A3480G A4769G C5742T C7028T A8860G G9055A T9698C A10398G A10550G T11299C A11467G A11470G G11719A G11914A A12308G G12372A C14167T C14766T T14798C T15074C A15326G A15924G C16278T T16311C

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Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Fri Jul 05, 2013 10:52 am
Gioiello wrote:From the paper of Cardoso posted by Gail T on anthrogenica we have:

JX297145 is interesting because probably is a new subclade of K1a1b1, perhaps with the Coding Region mutation 5742T. It has also the mutations 3107del, 16278T and a back mutation in 16224T!, already known from the Basque country.
We have on Mitosearch a Russian (from German descent), unfortunately tested only for HVRI, with 16224C.
Also this subclade of K1a1b1 is then European, like all the others, except the discussed Jewish K1a1b1a.



I am U5b2b and I have the mutation T16224C.

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PostPosted: Fri Jul 05, 2013 11:59 am
dartraighe wrote:
I am U5b2b and I have the mutation T16224C.


The mutation T16224C is stable in hg. K (I have all the three in HVRI yet: 16224C, 16311C and 16519C), but it is diffused in other haplogroups (or may be is the ancestral one not mutated: see RSRS of Behar 2012b). Remember that hg. K is linked with U, because it derives from U8b. These Basque haplotypes are strange, because are the unique to have massively had back mutations in 16224 and also in 16519.

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PostPosted: Fri Jul 05, 2013 7:44 pm
Gioiello wrote:From the paper of Cardoso posted by Gail T on anthrogenica we have:

JX297145 is interesting because probably is a new subclade of K1a1b1, perhaps with the Coding Region mutation 5742T. It has also the mutations 3107del, 16278T and a back mutation in 16224T!, already known from the Basque country.
We have on Mitosearch a Russian (from German descent), unfortunately tested only for HVRI, with 16224C.
Also this subclade of K1a1b1 is then European, like all the others, except the discussed Jewish K1a1b1a.

Hi Gioiello and all,

The Cardoso K1a1b1 sequence and the previous one from Gonzalez have three additional (beyond K1a1b1) mutations in common: 5742T, 16278T and a back mutation at 16224. The Gonzalez sequence has two more extras: 15074C and a back mutation at 16519. The Cardoso sequence has no "extra extras." (Ignore the 3107 deletion; that's the "phantom mutation" from the revision of the CRS.) The PhyloTree prefers to have three different sequences to declare a new subclade. It will sometimes add a subclade if it is defined by coding-region mutations and has two sequences with additional coding-region mutations, or maybe non-recurrent HVR mutations. In this case, only one sequence has additional mutations. My guess is that the reasoning behind this is that one sequence could possibly be incomplete. So, I would call this a new branch, but not a new subclade.

Bill Hurst

Posts: 2341
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
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MtDNA:
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PostPosted: Sat Jul 06, 2013 1:09 am
Bill Hurst wrote:
Gioiello wrote:From the paper of Cardoso posted by Gail T on anthrogenica we have:

JX297145 is interesting because probably is a new subclade of K1a1b1, perhaps with the Coding Region mutation 5742T. It has also the mutations 3107del, 16278T and a back mutation in 16224T!, already known from the Basque country.
We have on Mitosearch a Russian (from German descent), unfortunately tested only for HVRI, with 16224C.
Also this subclade of K1a1b1 is then European, like all the others, except the discussed Jewish K1a1b1a.

Hi Gioiello and all,

The Cardoso K1a1b1 sequence and the previous one from Gonzalez have three additional (beyond K1a1b1) mutations in common: 5742T, 16278T and a back mutation at 16224. The Gonzalez sequence has two more extras: 15074C and a back mutation at 16519. The Cardoso sequence has no "extra extras." (Ignore the 3107 deletion; that's the "phantom mutation" from the revision of the CRS.) The PhyloTree prefers to have three different sequences to declare a new subclade. It will sometimes add a subclade if it is defined by coding-region mutations and has two sequences with additional coding-region mutations, or maybe non-recurrent HVR mutations. In this case, only one sequence has additional mutations. My guess is that the reasoning behind this is that one sequence could possibly be incomplete. So, I would call this a new branch, but not a new subclade.

Bill Hurst


Perhaps it would be useful what I wrote last years and also now on anthrogenica:

(1/1)

Maliclavelli:
1386 16224C 16311C 16519C 073G 152C 263G 315.1C 497T
3073 16224C 16311C 16519C 073G 263G 315.1C 497T
3488 16224C 16311C 16519C 073G 263G 309.1C 315.1C 497T
7936 16224C 16311C 16519C 073G 263G 309.1C 309.2C 315.1C 497T

9438 16224C 16311C 16519C 073G 114T 200G 263G 315.1C 497T 522d 523d

3630 16278T 16311C 16519C 073G 263G 315.1C 497T
7683 16278T 16311C 16519C 073G 263G 315.1C 497T
8728 16278T 16311C 16519C 073G 263G 315.1C 497T

3878 16224C 16311C 16354T 16519C 073G 263G 309.1C 309.2C 315.1C 334C 497T 523.1C 523.2A

9698 16192T 16224C 16311C 16519C 073G 263G 315.1C497T 523.1C 523.2A


6808 16145A 16224C 16311C 16354T 16519C 073G 263G 309.1C 315.1C 497T 523.1C 523.2A

1450 16224C 16519C 073G 152C 263G 315.1C 497T 523.1C 523.2A 523.3C 523.4A
5814 16224C 16519C 073G 152C 263G 315.1C 497T 523.1C 523.2A 523.3C 523.4A
4026 16176T 16224C 16519C 073G 152C 263G 315.1C 497T 523.1C 523.2A 523.3C 523.4A

6441 16224C 16311C 16519C 073G 195C 263G 315.1C 497T 523.1C 523.2A 523.3C 523.4A

1507 16224C 16519C 073G 152C 263G 315.1C 497T 523.1C 523.2A
3068 16224C 16519C 073G 152C 263G 315.1C 497T 523.1C 523.2A
7368 16224C 16519C 073G 152C 263G 315.1C 497T 523.1C 523.2A 523.3C 523.4A


1803 16180G 16224C 16249C 16311C 16519.C 073G 263G 315.1C 408a 497T 523.1C 523.2A

1906 16224C 16234T 16311C 16519C 073G 146C 150T 263G 315.1C
5827 16224C 16234T 16311C 16519C 073G 146C 150T 263G 315.1C
8854 16224C 16234T 16311C 16519C 073G 146C 150T 263G 315.1C
8906 16224C 16234T 16311C 16519C 073G 146C 150T 263G 315.1C

2057 16150T 16224C 16311C 16519C 073G 146C 152C 263G 315.1C
7697 16224C 16311C 16519C 073G 146C 152C 263G 315.1C

7179 16224C 16311C 16519C 073G 146C 263G 315.1C 572T

2200 16086C 16278T 16311C 16519C 073G 263G 315.1C 497T

2605 16093C 16224C 16311C 16519C 073G 263G 315.1C 497T
7995 16093C 16224C 16311C 16519C 073G 263G 315.1C 497T

9193 16093C 16172C 16224C 16311C 16519C 073G 114T 152C 263G 315.1C 497T
9612 16093C 16172C 16224C 16311C 16519C 073G 114T 152C 263G 315.1C 497T

3825 16093C 16224C 16311C 16519C 073G 146C 152C 195C 263G 309.1C 315.1C 497T

6839 16093C 16224C 16311C 16519C 073G 263G 309.1C 315.1C 497T
6955 16093C 16224C 16311C 16519C 073G 263G 309.1C 315.1C 497T
8505 16093C 16224C 16311C 16519C 073G 263G 309.1C 315.1C 497T

2774 16261T 16278T 16311C 16519C 073G 263G 315.1C 497T

3057 16224C 16311C 16519C 073G 152C 263G 315.1C 497T 573d
5432 16224C 16311C 16519C 073G 152C 263G 315.1C 497T 573d
8424 16224C 16311C 16519C 073G 152C 263G 315.1C 497T

3108 16224C 16311C 16519C 073G 146C 152C 263G 315.1C 498d
3127 16224C 16311C 16519C 073G 146C 152C 263G 315.1C 498d
8762 16224C 16311C 16519C 073G 146C 152C 263G 315.1C 498d

5432 16145A 16224C 16311C 16519C 073G 146C 152C 263G 309.1C 315.1C 498d

8430 16224C 16311C 16519C 073G 146C 152C 263G 315.1C

7799 16224T 16311C 16319C 16463G 16519C 073G 152C 199C 263G 309.1C 315.1C 523.1C 523.2A

I have begun to collect the 45 hg.K from the paper «The Basque Paradigm: Genetic Evidence of a Maternal Continuity in the Franco-Cantabrian Region since Pre-Neolithic Times” (The American Journal of Human Genetics, vol. 90). Unfortunately the paper isn’t for free, but the supplements may be consulted and certainly we shall work to classify these haplotypes yet, but, at a first sight, I’d say that if hg.K isn’t born in the Franco-Cantabrian Refugium (or in Europe), I don’t know where all over the world it could be born.

But now I’d want to say something about this haplotype

1906 16224C 16234T 16311C 16519C 073G 146C 150T 263G 315.1C
5827 16224C 16234T 16311C 16519C 073G 146C 150T 263G 315.1C
8854 16224C 16234T 16311C 16519C 073G 146C 150T 263G 315.1C
8906 16224C 16234T 16311C 16519C 073G 146C 150T 263G 315.1C

found also in the paper of Maria LAURA Catelli et al., The impact of modern migrations on present-day multi-ethnic Argentina as recorded on the mitochondrial
DNA genome, “BMC Genetics 2011” and I spoke about on “Dienekes Anthropology blog”, here and in many private letters. The problem was if it is a K1a1b1a, as the authors said, and also the same author in a private letter, answering to my questions:

Dear Gioiello (CC: Carlos Vullo and Laura Catelli),
I go through your comments below;

1) How have you classified the haplotype 79 from Buenos Aires like a
K1a1b1a? It lacks the mutation 497T, not tested, and William Hurst
would classify it like K2b1 and I, for classifying it like a K1a, have
hypothesized a back mutation in 497 from T to the ancestral C, never
happened says W.Hurst.

Simply because it has transition at 16234 and any other position indicating other better candidate. I agree in that the classification is not very solid but it is to my view the most parsimonious one. It seems that some sub-branch of K1a1b1a could have an extra 114; which is not the case in #79 but it is in other Argentinean profiles. According to what we know from entire genome data, this profile is definitely not K2b1.
2) The other K1a1b1a-s are more certain: but it seem from Ashkenazi
Jews. I am searching for Italian K1a1b1a-s, because my theory is that
Ashkenazim derive (in part) from Italians converted during the Middle
Ages, but I should find some Italian K1a1b1a, being uncertain the true
origin of FTDNA 135366 K 16223T, 16224C, 16234T, 16311C, 16519C 73G,
114T, 263G, 315.1C, 497T. Your samples K1a1b1a-s were from Italians or
from Jews? And why have you used them to decide the ratio
Italian/Spanish mt in Argentine if they were Jews?
Our samples are “residents” in Argentina; they naturally speak Spanish and it is most likely that about half of them have about 50% Italian ancestry. Note however that Argentina has a huge Jews community. It is said that the third most important Jews community in America is in Argentina (first: USA and Canada). Note also that our paper is a meta-analysis and therefore, we have little information concerning the samples provided by others. A meta-analysis tries to minimize the effect of potential sampling biases in admixture estimates; we discuss about this in the article.

3) This is only an ascertainment: “Perhaps you are not interested to
other haplogroups, but in those data there are two interesting R0a1a1
and probably R0a2 with many mutations
in HVRI from the Italian Refugium, where surely R0a was, not in Middle
East”. Glad to see them, but after the paper of Achilli and some test I
did c/o FTDNA, also FTDNA has admitted it: “Mitochondrial haplogroup
R0a (formerly known as pre-HV1) is a primarily European haplogroup
that was present in Europe beginning approximately 20,000 years ago.
It occurs in very low frequency throughout Europe, and some descendant
lineages of the original haplogroup R0a appear in the Near East as a
result of migration. It was probably one of the original mitochondrial
haplogroups in Europe, and likely pre-dates the occurrence of farming
in Europe. Future work will better resolve the distribution and
historical characteristics of this haplogroup”.
Good to know; effectively, e.g. one of them (16126 16168 16264 16295 16362) is found in several Italian locations (including Sicily), but also in Turkey (Kurds, Anatolia).

4) Also an ascertainment is having found some links between some
haplotypes of your paper and some Italian ones: “And watch how close
is this Italian K1a with 1189 sample from San Juan: 16192T 16224C
16284G 16286G 16311C 16519C 073G 263G 309.1C 315.1C 497T
Mitosearch MGMSN from SMGF. How old is K1a in Italy!”
I don’t know!! A proper dating would require a good number of entire genomes...and founder analysis…
Regards,
A.S.
Maliclavelli:
14. DQ200804(Basque) Gonzalez K1a1b1 13-JUN-2006 A73G A263G 315.1C C497T A750G T1189C A1438G A1811G A2706G A3480G A4769G C5742T C7028T A8860G G9055A T9698C A10398G A10550G T11299C A11467G A11470G G11719A G11914A A12308G G12372A C14167T C14766T T14798C T15074C A15326G A15924G C16278T T16311C

This K1a1b1 Basque on the “Ian Logan spreadsheet” demonstrates once more that probably the Basque with this signature (16278T etc.)* are K1a1b1 and this sample has had beyond the back mutation of 16224 also that of 16519. Very interesting.

* 3630 16278T 16311C 16519C 073G 263G 315.1C 497T
7683 16278T 16311C 16519C 073G 263G 315.1C 497T
8728 16278T 16311C 16519C 073G 263G 315.1C 497T

PS. Now I 'd add also these haplotypes to these three:
2200 16086C 16278T 16311C 16519C 073G 263G 315.1C 497T
2774 16261T 16278T 16311C 16519C 073G 263G 315.1C 497T

Posts: 2341
Joined: Sun Mar 18, 2012 7:08 am
Location: Pisa (Italy)
YDNA:
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PostPosted: Sat Jul 06, 2013 2:15 am
Of course someone should test (FGS) these people:
1. 16224C Not Tested
2. 16278T
3. 16311C
4. 16519C
ID: 6TCK3
and the 5 Basques I cited above.

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